Hospitals in opposition-held parts of Syria are refusing to share GPS coordinates with Russian and Syrian authorities because of repeated attacks on medical facilities and workers, Médecins Sans Frontières and humanitarian workers on the ground have said.

International charity MSF said it took the decision not to formally inform Syria’s government or its Russian allies about the location of some medical facilities, such as the one hit by a deadly airstrike this week, amid concerns that doing so could make them targets.

Joanne Liu, MSF International president, told reporters in Geneva that deliberate attacks on civilian infrastructures were routine. “Healthcare in Syria is in the crosshair of bombs and missiles. It has collapsed,” Liu said. “Let me be clear: attacks on civilians and hospitals must stop. The normalisation of such attacks is intolerable.”

Humanitarian officials, speaking on condition of anonymity, told the Guardian that the Syrian government has explicitly threatened to bomb a hospital in a besieged suburb of Damascus if it continues to admit emergency cases, and said doctors and families were targeted by the regime.

“Since 2011 during the demonstration time, medical activities that are not under their control are considered by the government of Syria as illegal and consequently as legitimate targets,” one official said. “This decision explains the repeated threat, arrest, torture and killing of doctors … and their direct families in addition to the systematic targeting of networks in charge of supplying underground medical activities in besieged zones.”

“Given the number of hospitals that have been bombed since the war started, they do not think [giving GPS coordinates] is going to protect them, rather the opposite,” another official said.

An MSF facility in Idlib province, Syria, was attacked on 15 February 2016. Photograph: AP

The MSF-supported hospital was located in Idlib, a province entirely outside of government control and where only the Russian and Syrian air forces are carrying out raids.

Fourteen attacks against hospitals have already taken place since the beginning of this year, contradicting claims by Dmitry Medvedev, the Russian prime minister, that Russian forces are not targeting civilians or civilian infrastructure as part of its campaign to support the Assad government.

This week’s violence came just days after major powers reached a deal in Munich for a “cessation of hostilities” that is supposed to come into effect on Thursday night, but now appears as distant as ever.

“Over the past 15 days there has been a focus on northern Aleppo and almost all the hospitals in the area are out of service because they have been directly targeted,” said Mustafa Ajjaj, who runs a hospital in the town of Kafr Hamra in the area.

Aleppo has been the target of a major Russian-backed offensive aimed at severing rebel supply lines, and has sent tens of thousands of civilians fleeing to the Turkish border.

“They are directly targeting civilians and are completely focused on hospitals,” Ajjaj said. “In the beginning we thought it was simply indiscriminate, but there is repeated targeting of hospitals.”

“There is great danger in giving the [GPS] locations because the targeting of the hospitals is definite and clear and systematic,” he added.

Ajjaj said Aleppo now lacks a hospital capable of conducting surgical procedures as a consequence of government and Russian airstrikes. Those hospitals that haven’t been completely destroyed are only able to offer first aid before sending the wounded to the Turkish border, he added.

Humanitarian officials said a hospital in Moadamiyah, a suburb of Damascus under siege by the Assad regime, was told it would be targeted if it continued to accept emergency cases. The hospital replied saying it was a neutral party.

Zaidoun al-Zoubi, who heads the Union of Syrian Medical Relief Organisations, an outfit that runs 11 primary healthcare centres in Syria and the biggest hospital in the country’s north, said the government sees hospitals operating without its permission as legitimate targets. He estimated that around 150 medical facilities were hit in total last year.

“They are targeting hospitals specifically,” he said. “You give them GPS coordinates when you are worried about collateral damage. This is systematic.”

“I am ready to give them but I need guarantees that after providing these I will not be bombed,” he added.

As early as 2013, the UN independent commission of inquiry investigating alleged war crimes in Syria said attacks on medical facilities were being used systematically as a weapon of war by the Assad regime.

The attacks have continued unabated in recent months.

MSF said on Thursday that a total of 94 airstrikes and shelling attacks hit facilities supported by the organisation in 2015 alone, in 12 cases leading to the total destruction of the facility. Some hospitals also suffered from “double tap” attacks, where a second airstrike targets paramedics and EMTs who arrive at the scene to rescue the wounded, between 20-60 minutes after the first bombing.

“The medical facilities supported by MSF are particularly vulnerable as a result of a decision by the Syrian government in 2012 to declare as illegal any clinic providing medical care to victims of violence in opposition-controlled areas,” the organisation said in its report. “Consequently, the majority of the MSF-supported clinics have been forced to operate clandestinely in unmarked and undeclared locations.”

In February last year, the NGO Physicians for Human Rights said it had documented 224 attacks on 175 health facilities since the start of the conflict, and 599 medical personnel had been killed. Many humanitarian workers have been detained.

The attacks continued after the Russian intervention – the organisation documented at least 10 attacks by Russian aircraft on medical facilities in October alone, the first month of Russia’s aerial campaign.

The assault on healthcare goes beyond explicit attacks on medical facilities. A report last year by the Syrian-American Medical Society (Sams) interviewed 27 physicians and medical workers in Syria, including several who had been arrested, arbitrarily detained and tortured for treating members of the opposition.

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Ajjaj, the doctor in Aleppo, said doctors from regime-held areas who are moved to assist civilians in rebel-controlled territory do so anonymously for fear of reprisals against them and their families.

Zaher Sahloul, the former president of Sams, said: “In general doctors and nurses caught by the security forces in government controlled areas treating the injured from the other side are detained, tortured, killed, threatened or forced to flee. That is why 75% of all doctors in Syria left the country.”

“On the other hand, doctors and nurses in non-government controlled areas are bombed … by the regime barrel bombs and now by Russian jets.”